DESCRIPTION

This module is the engine behind the mok program. See mok(1) for a detailed description of the language. Mok is part of the PerlMol project, http://www.perlmol.org.

METHODS

Chemistry::Mok->new($code, %options)

Compile the code and return a Chemistry::Mok object. Available options:

package

If the package option is given, the code runs in the Chemistry::Mok::UserCode::$options{package} package instead of the Chemistry::Mok::UserCode::Default package. Specifying a package name is recommended if you have more than one mok object and you are using global varaibles, in order to avoid namespace clashes.

pattern_format

The name of the format which will be used for parsing slash-delimited patterns that don't define an explicit format. Mok versions until 0.16 only used the 'smiles' format, but newer versions can use other formats such as 'smarts', 'midas', 'formula_pattern', and 'sln', if available. The default is 'smarts'.

$mok->run($options, @args)

Run the code on the filenames contained in @args. $options is a hash reference with runtime options. Available options:

build_3d

Generate 3D coordinates using Chemistry::3DBuilder.

aromatize

"Aromatize" each molecule as it is read. This is needed for example for matching SMARTS patterns that use aromaticity or ring primitives.

delete_dummies

Delete dummy atoms after reading each molecule. A dummy atom is defined as an atom with an unknown symbol (i.e., it doesn't appear on the periodic table), or an atomic number of zero.

find_bonds

If set to a true value, find bonds. Use it when reading files with no bond information but 3D coordinates to detect the bonds if needed (for example, if you want to do match a pattern that includes bonds). If the file has explicit bonds, mok will not try to find the bonds, but it will reassign the bond orders from scratch.

format

The format used when calling $mol_class->read. If not given, $mol_class->read tries to identify the format automatically.

mol_class

The molecule class used for reading the files. Defaults to Chemistry::Mol.